This work presents a study of the assessment of the operating parameters of the catalytic wet peroxide oxidation (CWPO) of naproxen (NAP) using magnetite/multi-walled carbon nanotubes (Fe3O4/MWCNTs) as a catalyst. The effect of pH, temperature, and H2O2 dosage on CWPO process was evaluated by using the response surface model (RSM), allowing us to obtain an optimum NAP removal of 82% at the following operating conditions: pH = 5, T = 70°C, [H2O2]0 = 1.5 mM, and [NAP]0 = 10.0 mg/L. Therefore, NAP degradation kinetics were revealed to follow a pseudo-second-order kinetic model, and an activation energy value of 4.75 kJ/mol was determined. Adsorption and using only H2O2 experiments, both considered as blank tests, showed no significant removal of the pollutant. Moreover, Fe3O4/MWCNTs material exhibited good recyclability along three consecutive cycles, finding an average NAP removal percentage close to 80% in each cycle of 3 h reaction time. In addition, the scavenging tests confirmed that the degradation of NAP was mainly governed by •OH radicals attack. Two reaction sequences were proposed for the degradation mechanism according to the detected byproducts. Finally, the versatility of the catalyst was evidenced in the treatment of different environmentally relevant aqueous matrices (wastewater treatment plant effluent (WWTP), surface water (SW), and a hospital wastewater (HW)) spiked with NAP, obtaining total organic carbon (TOC) removal efficiencies after 8 h in the following order: NAP-SW > NAP-HW > NAP-WWTP.